5i*^dZddlmZmZmZmZddlZddlZddlm Z ddl m Z Gdde Z y)z DXAnalysis Handler ++++++++++++++++++ Analyses are DNAnexus entities that capture an instantiation of a running workflow. They can be created from :func:`dxpy.bindings.dxworkflow.DXWorkflow.run` or from an existing analysis ID. )print_functionunicode_literalsdivisionabsolute_importN)DXObject)DXJobFailureErrorcReZdZdZdZd dZd dZdZdZdZ dd Z d Z dd Z d Z y) DXAnalysisz) Remote analysis object handler. analysisNcbd|_tj|||j|y)N)dxid)_test_harness_resultr__init__set_id)selfr s z/home/marpiech/ifpan-abm-pgxpred/analysis/marpiech-gwas-test/venv/lib/python3.12/site-packages/dxpy/bindings/dxanalysis.pyrzDXAnalysis.__init__.s&$(!$T* Dc i}|||d<tjj|j|fi||_|jS)az :param fields: dict where the keys are field names that should be returned, and values should be set to True (by default, all fields are returned) :type fields: dict :returns: Description of the analysis :rtype: dict Returns a hash with key-value pairs containing information about the analysis fields)dxpyapianalysis_describe_dxid_desc)rrkwargsdescribe_inputs rdescribezDXAnalysis.describe3sD  '-N8 $XX// NUfU zzrc ^tjj|jd|ifi|y)z :param tags: Tags to add to the analysis :type tags: list of strings Adds each of the specified tags to the analysis. Takes no action for tags that are already listed for the analysis. tagsN)rranalysis_add_tagsrrrrs radd_tagszDXAnalysis.add_tagsFs% ""4::~HHrc ^tjj|jd|ifi|y)z :param tags: Tags to remove from the analysis :type tags: list of strings Removes each of the specified tags from the analysis. Takes no action for tags that the analysis does not currently have. rN)rranalysis_remove_tagsrr!s r remove_tagszDXAnalysis.remove_tagsRs% %%djj64.KFKrc ^tjj|jd|ifi|y)a :param properties: Property names and values given as key-value pairs of strings :type properties: dict Given key-value pairs in *properties* for property names and values, the properties are set on the analysis for the given property names. Any property with a value of :const:`None` indicates the property will be deleted. .. note:: Any existing properties not mentioned in *properties* are not modified by this method. propertiesN)rranalysis_set_propertiesr)rr'rs rset_propertieszDXAnalysis.set_properties^s' ((lJ5OZSYZrc d} |jd i|}|dk(ry|dvrl|jd i|}djd i|}|jddk7r)|dd|dk7r|dj|dd z }t ||d k(r t d ||k\s|dkr t d t j |||z })a :param interval: Number of seconds between queries to the analysis's state :type interval: integer :param timeout: Maximum amount of time to wait, in seconds, until the analysis is done (or at least partially failed) :type timeout: integer :raises: :exc:`~dxpy.exceptions.DXError` if the timeout is reached before the analysis has finished running, or :exc:`~dxpy.exceptions.DXJobFailureError` if some job in the analysis has failed Waits until the analysis has finished running. rdone)failedpartially_failedz@Analysis has failed because of {failureReason}: {failureMessage} failureFromNidz (failure from {id}))r/ terminatedzAnalysis was terminated.z8Reached timeout while waiting for the analysis to finish) _get_staterformatgetrtimesleep)rintervaltimeoutrelapsedstatedescerr_msgs r wait_on_donezDXAnalysis.wait_on_doneos#DOO-f-E66$t}}.v.c\cckfjk88M*d2tM7J47PTXY]T^7^5<<]@STX@Y<ZZG'00 $'(BCC'!Wq['(bcc JJx x G#rc Xtjj|jfi|y)z5 Terminates the associated analysis. N)rranalysis_terminaterrrs r terminatezDXAnalysis.terminates ##DJJ9&9rcPd|j|di}|||dd<|||dd<|S)a9 :param field: Output field name of this analysis :type field: string :param index: If the referenced field is an array, optionally specify an index (starting from 0) to indicate a particular member of the array :type index: int :param metadata: If the referenced field is of a data object class, a string indicating the metadata that should be read, e.g. "name", "properties.propkey", "details.refgenome" :type metadata: string Returns a dict containing a valid reference to an output of this analysis. z$dnanexus_link)r fieldindexmetadata)r)rrCrDrElinks rget_output_refzDXAnalysis.get_output_refsH!tzzE"JK  .3D! "7 +  19D! ": . rc D|jddtdi|dS)z :returns: State of the remote object :rtype: string Queries the API server for the analysis's state. Note that this function is shorthand for: dxanalysis.describe(**kwargs)["state"] rT)r:r:r1)rdictr@s rr2zDXAnalysis._get_states't}}?Dt$4??HHr)N)i: )NN)__name__ __module__ __qualname____doc___classrrr"r%r)r=rArGr2r1rrr r 's?F & I L[" >: & Irr ) rN __future__rrrrr5r dxpy.bindingsrdxpy.exceptionsrr r1rrrSs/" SR &- MIMIr